Commit 3733e77b authored by Sylvain Jasson's avatar Sylvain Jasson
Browse files

Parameters to makefile - outputs samples

parent dcb304da
EXAMPLE_DIR = ~/INSTALL_DIR/SPELL_TEST/spell_qtl-0.1-alpha.1-Linux/share/spell-qtl/examples/three_parents_F2
BINDIR = /home/sjasson/INSTALL_DIR/SPELL_TEST/spell_qtl-0.1-alpha.1-Linux/bin
SRCDIR = /home/sjasson/dev/spel
EXAMPLE_DIR = $(SRCDIR)/examples/three_parents_F2
user_manual.pdf : spell-pedigree.tex spell-marker.tex spell-qtl.tex spell-qtl-examples.tex version.tex user_manual.tex images/Spell-pipeline2.svg inputs outputs
pdflatex --shell-escape user_manual.tex && pdflatex --shell-escape user_manual.tex
......@@ -6,20 +10,20 @@ user_manual.pdf : spell-pedigree.tex spell-marker.tex spell-qtl.tex spell-qtl-ex
version.tex :
git tag | tail -1 > version.tex
spell-pedigree.tex : ../man/spell-pedigree.1.md
/usr/bin/pandoc ../man/spell-pedigree.1.md --listings -f markdown -t latex -o spell-pedigree.tex
spell-pedigree.tex : $(SRCDIR)/doc/man/spell-pedigree.1.md
/usr/bin/pandoc $(SRCDIR)/doc/man/spell-pedigree.1.md --listings -f markdown -t latex -o spell-pedigree.tex
sed -i s/\\label\{/\label\{spell-pedigree:/g spell-pedigree.tex
spell-marker.tex : ../man/spell-marker.1.md
/usr/bin/pandoc ../man/spell-marker.1.md --listings -f markdown -t latex -o spell-marker.tex
spell-marker.tex : $(SRCDIR)/doc/man/spell-marker.1.md
/usr/bin/pandoc $(SRCDIR)/doc/man/spell-marker.1.md --listings -f markdown -t latex -o spell-marker.tex
sed -i s/\\label\{/\label\{spell-marker:/g spell-marker.tex
spell-qtl.tex : ../man/spell-qtl.1.md
/usr/bin/pandoc ../man/spell-qtl.1.md --listings -f markdown -t latex -o spell-qtl.tex
/usr/bin/pandoc $(SRCDIR)/doc/man/spell-qtl.1.md --listings -f markdown -t latex -o spell-qtl.tex
sed -i s/\\label\{/\label\{spell-qtl:/g spell-qtl.tex
spell-qtl-examples.tex : ../man/spell-qtl-examples.1.md
/usr/bin/pandoc ../man/spell-qtl-examples.1.md --listings -f markdown -t latex -o spell-qtl-examples.tex
spell-qtl-examples.tex : $(SRCDIR)/doc/man/spell-qtl-examples.1.md
/usr/bin/pandoc $(SRCDIR)/doc/man/spell-qtl-examples.1.md --listings -f markdown -t latex -o spell-qtl-examples.tex
sed -i s/\\label\{/\label\{spell-qtl-examples:/g spell-qtl-examples.tex
......@@ -32,9 +36,9 @@ inputs :
outputs :
spell-pedigree -wd my_directory -n my_name -p $(EXAMPLE_DIR)/example1.ped
spell-marker -wd my_directory -n my_name -m F2:A/B $(EXAMPLE_DIR)/example1_F2.gen -m F2C:A/C $(EXAMPLE_DIR)/example1_F2C.gen -o F2,F2C -O1
#spell-qtl -wd my_directory -n my_name -p F2 $(EXAMPLE_DIR)/example1_F2.phen -p F2C $(EXAMPLE_DIR)/example1_F2C.phen -gm $(EXAMPLE_DIR)/example1.map -P auto QTL-detection CIM connected
$(BINDIR)/spell-pedigree -wd my_directory -n my_name -p $(EXAMPLE_DIR)/example1.ped
$(BINDIR)/spell-marker -wd my_directory -n my_name -m F2:A/B $(EXAMPLE_DIR)/example1_F2.gen -m F2C:A/C $(EXAMPLE_DIR)/example1_F2C.gen -o F2,F2C -O1 -Op
$(BINDIR)/spell-qtl -wd my_directory -n my_name -p F2 $(EXAMPLE_DIR)/example1_F2.phen -p F2C $(EXAMPLE_DIR)/example1_F2C.phen -gm $(EXAMPLE_DIR)/example1.map output-nppop
clean:
rm -f *.aux *.log *.pdf *.toc *.out *.lol
......
......@@ -458,22 +458,34 @@ General output directory organization is :
%s sep=12pt,
before computing xy={l=20pt},
}
[my\_directory
[my\_name.1-point
[my\_directory \textsl{(directory)}
[my\_name.1-point \textsl{(directory)}
[my\_name.pedigree-and-probabilities.M\_1\_10.csv \textsl{(text file)} ]
[...]
]
[my\_name.cache
[my\_name.spell-marker.data]
[my\_name.spell-pedigree.data]
[...]
[my\_name.cache \textsl{(directory)}
[my\_name.spell-marker.data \textsl{(binary file)}]
[my\_name.spell-pedigree.data \textsl{(binary file)}]
]
[my\_name.n-point
[...]
[my\_name.n-point \textsl{(directory)}
[ch1 \textsl{(directory)}
[F2 \textsl{(directory)}
[my\_name.ch1.F2.0.csv \textsl{(text file)}]
[...]
]
[F2C \textsl{(directory)}
[my\_name.ch1.F2.0.csv \textsl{(text file)}]
[...]
]
]
[ch2 \textsl{(directory)}
[...]
]
]
[my\_name.report
[my\_name.report \textsl{(directory)}
[...]
]
[my\_name.spell-qtl.log
[my\_name.spell-qtl.log \textsl{(text file)}
]
]
\end{forest}
......@@ -484,8 +496,8 @@ General output directory organization is :
\item A configuration name using command line option \texttt{-n my\_name} or \texttt{--name my\_name} is used to name subdirectories.
\item Parental Origin Probabilities are output as CSV files
\begin{description}
\item [1-point] one file per marker (with pedigree like structure),
\item [n-point] one file per linkage group per generation per individual
\item [1-point] one file per marker (with pedigree like structure), use option \texttt{-O1} in command \texttt{spell-marker} to output these files
\item [n-point] one file per linkage group per generation per individual, use model option \texttt{output-nppop} in command \texttt{spell-qtl} to output these files.
\end{description}
\item a report containing
\begin{itemize}
......@@ -498,12 +510,6 @@ General output directory organization is :
\section{Output files samples}
\subsection{1-point POP}
%\lstinputlisting[%numbers=left,
%frame=single,
%breaklines=false,
%caption={[1-point output file] 1-point output file (selected lines from my\_name.pedigree-and-probabilities.M_1_1.csv from my\_directory/my\_name.1-point/)},
%linerange={1-12,107-112}
% ]
\lstinputlisting[numbers=left,
frame=single,
caption={[1-point output file] 1-point output file (selected lines from file \texttt{my\_name.pedigree-and-probabilities.M\_1\_1.csv} in directory \texttt{my\_directory/my\_name.1-point/} ) },%(selected lines from my\_name.pedigree-and-probabilities.M_1_1.csv from my\_directory/my\_name.1-point/)},
......@@ -512,6 +518,8 @@ General output directory organization is :
Note that you must use \texttt{-01} command line option in \texttt{spell-marker} in order to generate these files.
\subsection{n-point POP}
\begin{appendices}
......
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